Package picard.sam.markduplicates
Class CheckDuplicateMarking
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.markduplicates.CheckDuplicateMarking
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@DocumentedFeature(enable=false) public class CheckDuplicateMarking extends CommandLineProgram
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CheckDuplicateMarking.Mode
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Field Summary
Fields Modifier and Type Field Description File
INPUT
CheckDuplicateMarking.Mode
MODE
File
OUTPUT
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CheckDuplicateMarking()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(doc="Input BAM or SAM file to check.", shortName="I") public File INPUT
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OUTPUT
@Argument(doc="Output file into which bad querynames will be placed (if not null).", shortName="O", optional=true) public File OUTPUT
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MODE
@Argument(doc="Which reads of the same name should be checked to have same duplicate marking.") public CheckDuplicateMarking.Mode MODE
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Method Detail
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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